Amid the escalated diplomatic row between Turkey and the United States, mixed voices emerging from the Pentagon and U.S. State Department have sparked confusion in Ankara.

The Pentagon said on Tuesday that military cooperation between the two states has not been affected by the recent incidents.

Pentagon spokesman Col. Robert Manning told reporters: "I can confirm that these developments have not impacted our operations or personnel."

Manning said that "the Turkish Air Force Base in İncirlik continues to fulfill an important role supporting NATO and coalition efforts," adding the U.S. would continue to coordinate joint operations with Ankara as Turkey is a close ally.

Commenting on the recent crisis, Justice and Development Party (AK Party) spokesman Mahir Ünal said: "The U.S. suspending of visa services is not sustainable for both countries [and] we hope that it will not affect military operations."

Relations between Ankara and Washington recently hit a new low as the two countries mutually suspended visa services.

The decision to suspend all non-immigrant visa services at diplomatic facilities first came from the U.S. releasing a statement that said: "The recent events have forced the U.S. government to reassess the commitment of the government of Turkey to the security of U.S. Mission Facilities and personnel."

The U.S. was referring to the arrestment of a consulate employee on charges of having links to the Gülenist Terror Group (FETÖ). Following the U.S. decision, Ankara announced that it also suspended visa services to U.S. citizens in retaliation.

Yaşar Hacısalihoğlu, rector of Yeni Yüzyıl University, contended that the U.S. contradicted its own values with the decision to suspend the visa services, and added: "As there were no violations of law regarding the arrest of the person and all the necessary proof was provided, Washington should not have taken that step."

Murat Yeşiltaş, an academic from Sakarya University, told Daily Sabah that in some cases, political crisis do not affect military cooperation, pointing to the U.S.'s compartmentalization of relations in political and military issues, which are challenging.

"The statement from the Pentagon might be considered as a message to both sides not to increase tension further," Yeşiltaş said.

He said that the U.S. recognizes the significance of Turkey, not only for İncirlik Air Base, but also for its role in an environment where the U.S. is fighting Daesh and struggling to secure the stability of Iraq.

Touching on the different messages coming from the Pentagon and the State Department, Yeşiltaş said: "In relations with the U.S., the political and military stance on an issue might converge or differ from time to time."

Nurşin Güney, an academic from Yıldız Technical University, told Daily Sabah: "Even though there are some political issues between the two countries, there are no changes in military relations."

In reference to the compartmentalization of the relations, Yeşiltaş said that even though Turkey strongly criticizes the U.S. support for some "terrorist organizations," İncirlik Air Base continue to function.

As there has been no high-level comment on the visa situation from Washington, Yeşiltaş predicted that diplomacy will will be used to resolve the conflict.

Referring to Prime Minister Binali Yıldırım's statements that the issue needs to be solved in the background, Güney stressed the significance of using diplomacy and added that further escalation of the conflict would not benefit anyone.

Meanwhile, Hacısalihoğlu highlighted Turkey's stance in relations: "Turkey has been stressing the relations as allied countries and reiterates that the fight against terrorism cannot be achieved by using another one. Ankara's main expectation is to have symmetric relations based on the international law and mutual respect."

According to Hacısalihoğlu, while Turkey expects support from its allies in its fight against terrorist groups, it faces a negative stance. He said that the ups and downs in U.S. foreign policy have been reflected in its political stance regarding FETÖ.